Computational protocol: Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae)

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Protocol publication

[…] Sequences were edited and aligned by eye with BioEdit ver7.0.4.1 []. Sequences were checked against goby control region sequences on GenBank, with a tblastx search, to ensure that the correct region was amplified. Haplotypes were identified in Collapse1.2 http://darwin.uvigo.es. Haplotype (h) and nucleotide diversity (π) indices were calculated for each population individually and for the whole dataset, in Arlequin3.1 []. All haplotypes have been deposited in [GenBank: EU335086–EU335140]. [...] Analysis of Molecular Variance (AMOVA) was carried out in Arlequin3.1 to investigate the geographical distribution of haplotypes and provide the fixation indices for between- and within population variation. ΦST values were calculated to take the number of mutational changes between the haplotypes into consideration []. SAMOVA was used to calculate the geographic distribution of genetic structure. This maximises the proportion of the total genetic variation between groups of populations, as well as identifying possible genetic barriers between them, without pre-defining populations as is necessary for AMOVA []. The geographical coordinates of each sampling location were obtained from Google Earth®. To detect possible isolation by distance, a Mantel test was performed in Arlequin3.1 using 10 000 permutations and the measured geographical distances between localities determined from a scaled map as the shortest land-sea interface distance, but excluding bays. […]

Pipeline specifications

Software tools BioEdit, TBLASTX, Arlequin, SAMOVA
Applications Phylogenetics, Population genetic analysis, Nucleotide sequence alignment
Organisms Drosophila melanogaster